[gmx-users] lincs contraint failure

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 28 00:42:50 CET 2006

Nuri A Temiz wrote:
> Dear Mark
> The mdp file is how it should be. I also did a cut-off run from the same 
> starting point and it runs. 
> For the PME i have tried to decrase the time step to 1 fs. that did not work
> either. The protein is exploding and simulations is crashing. 

OK. Take your cutoff and PME .tpr files and compare them. The simplest 
thing to do is to "gmxdump -s cutoff.tpr > cutoff.txt" and similarly for 
PME. Then use diff to compare them. This will make absolutely clear 
whether you are doing the same thing with different electrostatic 
treatment or not. Also visualize the exploding and non-exploding runs to 
see if that enlightens you.


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